feat(storage): move desktop SQLite ownership into a storage utility process

Main no longer opens desktop business SQLite. A single utility-process
storage owner holds the Assistant, Knowledge, attachment, document-result,
remote-binding and native model-ledger databases and runs whole domain
transactions; Main and Runtime callers use explicit async domain operations.

- Remove the Main readWithFallback path and the supervision worker's
  separate business write connection; manifests are scanned read-only and
  committed by the sole writer.
- Remote events are ACKed only after commit; process loss reports
  unconfirmed writes instead of replaying them.
- Use native utilityProcess messaging with one in-flight bound (32) and
  ordered waiting instead of capacity rejection and retries.
- Start the storage process before the window so startup overlaps.
- Keep short tool output in memory and store full output once in owned
  storage; paging, branching, restart and deletion reuse that copy.
- Put required runtime launch files under goodbuddy-prefixed owned temp
  directories and reclaim confirmed stale ones; stop writing duplicate
  parsed.md.
- Add lint guards for SQLite ownership and architecture, concurrency
  acceptance fixtures, and maintenance/architecture documentation.

Validation: typecheck and lint pass. Alternating baseline (edf019aa) vs
candidate runs show no regression on single-session, C01, C02, C04 and a
5-minute C06; Main p99 drops from ~21 ms to ~16.7 ms under concurrency.
Fresh portable copy (1.75M events) upgrade content unchanged; real-model
output paging passes with 4 external requests. Full npm test runs had
1-9 different timing-sensitive failures per run that pass when rerun.
Not covered: C03 review publication, C07 source body, app-level C05.

src/main/knowledge/knowledge-embedding-index-repository.ts

@@ -3,21 +3,26 @@ import type {
   EmbeddingIndexRecord,
   EmbeddingIndexRepository
 } from './embedding-index-coordinator'
-import type { KnowledgeDatabase } from './knowledge-database'
+import type { KnowledgeStoragePort } from './knowledge-storage-port'
 
 export class KnowledgeEmbeddingIndexRepository
 implements EmbeddingIndexRepository {
   constructor(
-    private readonly database: KnowledgeDatabase,
+    private readonly database: Pick<KnowledgeStoragePort,
+      'getLastEmbeddingIndexJob' | 'saveEmbeddingIndexJob' |
+      'listEmbeddingIndexDocumentIds' | 'getEmbeddingIndexDocument' |
+      'beginDocumentEmbeddingReplacement' | 'appendDocumentEmbeddingBatch' |
+      'finishDocumentEmbeddingReplacement' | 'discardDocumentEmbeddingReplacement' |
+      'recordEmbeddingIndexError'>,
     private readonly knowledgeBaseId: string
   ) {}
 
   async getLastJob(): Promise<EmbeddingIndexStatus['job']> {
-    return this.database.getLastEmbeddingIndexJob(this.knowledgeBaseId)
+    return await this.database.getLastEmbeddingIndexJob(this.knowledgeBaseId)
   }
 
   async saveStatus(status: EmbeddingIndexStatus): Promise<void> {
-    this.database.saveEmbeddingIndexJob(
+    await this.database.saveEmbeddingIndexJob(
       this.knowledgeBaseId,
       status.job
     )
@@ -26,7 +31,7 @@ implements EmbeddingIndexRepository {
   async listIndexDocumentIds(signal: AbortSignal) {
     signal.throwIfAborted()
     const documentIds =
-      this.database.listEmbeddingIndexDocumentIds(
+      await this.database.listEmbeddingIndexDocumentIds(
         this.knowledgeBaseId
       )
     signal.throwIfAborted()
@@ -39,7 +44,7 @@ implements EmbeddingIndexRepository {
   ) {
     signal.throwIfAborted()
     const document =
-      this.database.getEmbeddingIndexDocument(documentId)
+      await this.database.getEmbeddingIndexDocument(documentId)
     signal.throwIfAborted()
     return document
   }
@@ -52,12 +57,11 @@ implements EmbeddingIndexRepository {
   ): Promise<string> {
     signal.throwIfAborted()
     const replacementId =
-      this.database.beginDocumentEmbeddingReplacement(
+      await this.database.beginDocumentEmbeddingReplacement(
         documentId,
         provider,
         model
       )
-    signal.throwIfAborted()
     return replacementId
   }
 
@@ -70,7 +74,7 @@ implements EmbeddingIndexRepository {
     signal: AbortSignal
   ): Promise<void> {
     signal.throwIfAborted()
-    this.database.appendDocumentEmbeddingBatch(
+    await this.database.appendDocumentEmbeddingBatch(
       replacementId,
       documentId,
       provider,
@@ -92,19 +96,18 @@ implements EmbeddingIndexRepository {
     signal: AbortSignal
   ): Promise<void> {
     signal.throwIfAborted()
-    this.database.finishDocumentEmbeddingReplacement(
+    await this.database.finishDocumentEmbeddingReplacement(
       replacementId,
       documentId,
       provider,
       model
     )
-    signal.throwIfAborted()
   }
 
   async discardDocumentReplacement(
     replacementId: string
   ): Promise<void> {
-    this.database.discardDocumentEmbeddingReplacement(
+    await this.database.discardDocumentEmbeddingReplacement(
       replacementId
     )
   }
@@ -115,7 +118,7 @@ implements EmbeddingIndexRepository {
     model: string,
     error: string
   ): Promise<void> {
-    this.database.recordEmbeddingIndexError(
+    await this.database.recordEmbeddingIndexError(
       documentId,
       provider,
       model,